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DROSERA ROTUNDIFOLIA DIET DETERMINATION USING DNA DATA by 1,2 2 2,3 BARBORA LEKESYTE , STEPHEN KETT and MARTIJN J.T.N

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DROSERA ROTUNDIFOLIA DIET DETERMINATION USING DNA DATA by 1,2 2 2,3 BARBORA LEKESYTE , STEPHEN KETT and MARTIJN J.T.N Journal of the Lundy Field Society, 6, 2018 WHAT’S ON THE MENU: DROSERA ROTUNDIFOLIA DIET DETERMINATION USING DNA DATA by 1,2 2 2,3 BARBORA LEKESYTE , STEPHEN KETT AND MARTIJN J.T.N. TIMMERMANS 2Department of Natural Sciences, Middlesex University, The Burroughs, Hendon, London, NW4 4BT 3Department of Life Science, Natural History Museum, Cromwell Road, London, SW7 5BD 1Corresponding author, e-mail: [email protected] ABSTRACT The round-leaved sundew, Drosera rotundifolia, is a carnivorous plant species. On Lundy it is found in the nutrient-poor bog environments of Pondsbury and the northernmost quarry, where it supplements its diet with invertebrate prey. To gain insight into the diet of these two sundew populations a metabarcoding approach was trialled. This is, to our knowledge, the first study to use DNA barcodes to identify Drosera prey. At each site, a 0.25m2 quadrat was placed in a representative Drosera patch and two days’ worth of prey were collected. To identify prey items, Cytochrome c oxidase subunit I (COX1) sequences were obtained and compared to the Barcode of Life database. This revealed that Lundy sundews have a mixed diet. In total at least 20 different prey taxa were detected in the two 0.25m2 areas sampled. Sixteen taxa could be identified to species, indicating that metabarcoding permits accurate species level identification of sundew prey items. The majority of prey taxa were dipterans (two-winged flies), of which several have previously been reported on Lundy. Most prey taxa were detected in only one of the two quadrats examined (Jaccard’s index of Similarity=0.01; ‘dissimilar’). This might indicate that the two Drosera populations feed on distinct prey communities, but more research is needed to confirm this. Keywords: Lundy, carnivorous plants, sundew Drosera, DNA barcodes, prey taxa, Diptera INTRODUCTION Carnivorous plants of the genus Drosera (sundews) are typically found in nutrient poor environments (Ellison and Gotelli, 2001). They thrive under these deprived conditions by supplementing their diet with arthropod prey (Millett et al., 2003). Prey are caught and digested with modified leaves (‘blades’). Blades possess large numbers of glandular ‘hairs’ that secrete drops of viscous adhesive solution. When arthropods contact with - 55 - Journal of the Lundy Field Society, 6, 2018 these drops they are trapped and die (Adlassnig et al., 2010) (Figure 1). Digestive enzymes produced by the plants then dissolve prey items, releasing nutrients to be absorbed by the plant (Adamec, 2002). Figure 1: Drosera rotundifolia with prey items. © S. Kett The genus Drosera has attracted scientific attention since the eighteenth century, most of which focussed on benefits of prey capture on plant growth and survival (e.g. ‘Botany’, 1874; Darwin, 1875; Roth, 1782; Thum, 1988; Hooker, 1916). For example, Thum (1988) showed that artificially increased food supply Drosera increases dry weight, flower and leaf number and the overall trapping area of individual plants. Equally, plant traits (Foot et al., 2014) and microhabitat (Thum, 1986) have also been shown to affect prey capture efficiency and diet composition. Investigating natural Drosera diet, via morphological identification of prey, however, is often hampered by the rapid digestion of prey tissue. To overcome this difficulty a DNA barcoding approach to identify prey was trialled. DNA barcodes are standardised genetic markers used for taxonomic identification, ideally to species level (Hebert et al., 2003). DNA sequences are obtained from specimens and then compared to sequences from accurately identified and vouchered specimens in a reference database. Matches between ‘unknown’ DNA sequences and sequences in the database result in a positive identification for specimens of interest. This study focussed on the round-leaved sundew, D. rotundifolia L., Lundy’s only carnivorous plant species. Samples were taken from two populations (Figure 2). One population is found at the edge of Lundy’s largest pond, Pondsbury (51°10'38"N, 4°40'12"W). Much of the surface vegetation in this area is Sphagnum bog with frequent tussocks of Juncus sp. The other population is found in the northernmost quarry (51°10'45"N, 4°39'53"W). Here vegetation is characterised by Sphagnum and other plants adapted to acid, poorly drained soils. This study aimed to test whether sundew prey items can be identified to species level using molecular barcoding and to compare obtained identifications to existing Lundy species records. - 56 - Journal of the Lundy Field Society, 6, 2018 Figure 2: The two Lundy Drosera rotundifolia populations sampled. A) Pondsbury, B) the northernmost quarry. © B. Lekesyte MATERIAL AND METHODS Field work methods In June 2016, 0.5×0.5 m quadrats were established within the Pondsbury and Quarry D. rotundifolia populations. Quadrats were placed in locations judged ‘typical’ of a dense Drosera ‘patch’. Flags were used to indicate the four quadrat corners to permit relocation of each quadrat. On the first day of the experiment, plant blades were ‘cleaned’ using forceps to remove all prey items. To determine prey composition, prey were collected two days after cleaning occurred. Collected prey items were stored in tubes of absolute ethanol. Laboratory methods For each quadrat, prey samples were pooled in a single tube. DNA extractions were performed on these pooled samples. Ethanol was removed by pipetting. A heating block (56°C) was used to evaporate residual ethanol. DNA extractions used the Blood and Tissue Kit (Qiagen) and followed manufacturer’s recommendations, except that double volumes were used for buffer ATL, buffer AL and 100% ethanol. Extracted DNA was subsequently sent to NatureMetrics Ltd for metabarcoding. Metabarcoding followed NatureMetrics Ltd standard procedures. In brief, a short fragment of the cytochrome oxidase c subunit 1 (COI) barcode was amplified using primer Fol-degen-rev 5’- - 57 - Journal of the Lundy Field Society, 6, 2018 TANACYTCNGGRTGNCCRAARAAYCA-3’ (Yang et al. 2012) combined with Leray primer mlCOIintF: 5’-GGWACWGGWTGAACWGTWTAYCCYCC-3’ (Leray et al. 2013) or combined with primer ‘Short2’ 5’-CCNGAYATRGCNTTYCCNCG-3’ (NatureMetrics Ltd, pers. comm.) (Figure 3). All PCR reactions were performed in triplicate. PCR products were purified and quantified (Qubit high sensitivity kit). PCR products for the same site (quadrat) were pooled and Next Generation Sequencing (NGS) libraries were prepared as specified by Illumina for amplicon sequencing on the Illumina MiSeq System (Illumina Inc. 2013) and sequenced using an Illumina MiSeq 2×300 kit. Figure 3: Two fragments of the COX1 gene were amplified using PCR. Primers Short2 and Fol-degen-rev amplify a 365bp fragment. Primers mlCOIintF and Fol-degen-rev a 464bp fragment. Positions of the three primers (green triangles) on the COX1 gene sequence (green bar) are given Bioinformatic methods Raw sequencing reads for each site were stitched using PEAR (Zhang et al., 2014) and subsequently split by forward primer sequence using cutadapt (Martin, 2011). This step also trimmed uninformative PCR primer sequences. Low quality sequences were removed using the prinseq-lite Perl script (Schmieder and Edwards, 2011), removing all sequences that contained at least a single ‘N’, had a single position with a Phred quality below 20 and an average Phred quality below 30. Sequences were then converted to FASTA format using fq2fa (Peng et al., 2012). Operational Taxonomic Units (OTUs) were constructed from these files using the UPARSE pipe-line (Edgar, 2013). Sequences were de-replicated (merging all exact duplicates) and singletons (sequences that were observed once only) were removed. Remaining sequences were clustered at 97% similarity in USEARCH (Edgar, 2010) to generate OTUs and all sequences were subsequently assigned to each of the different OTUs (again at 97% similarity). OTUs with less than 10 sequences for both quadrats combined were discarded. To identify OTUs in the final dataset, sequences were compared to the Barcode of Life (BOLD) database (http://www.boldsystems.org/). Identifications were compared to the Diptera checklist for Lundy (Lane, 1977) and various other sources (Figure 4). Prey taxon approximate sizes were obtained from a variety of generic sources. Jaccard's Index of Similarity Jaccard's Index of Similarity was used to determine overall similarity of composition between the two sets of identified prey taxa, from the Pondsbury and the quarry sites. It was applied only where prey taxon presence could be unequivocally determined, e.g. if a genus occurs in both prey sets, it was not possible to determine without species identification whether a species level difference occurred between the two taxa. - 58 - Journal of the Lundy Field Society, 6, 2018 Figure 4: Taxa observed at two sites on Lundy using: Left) Leray (2013) primers and Right) Short2 (NatureMetrics Ltd., pers. comm.) primers. Left vertical axis: Number of sequences observed for a specific taxon. Blue (Pondsbury) and red (Quarry) bars and blue and red numbers on the graph represent number of sequences observed. Right axis: % similarity (grey bar) to a reference sequence in the BOLD database. Horizontal line indicates 97% similarity. Family names are given above graph. All families belong to Diptera, except *) Entomobryomorpha (Collembola), **) Opiliones (Arachnida) and ***) Araneae (Arachnida). Species names (if available) are given below graph. Numbers between parentheses refer to: 1) (Lane, 1978) 2) (Menzel et al., 2006) 3) (Smith
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